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Flashcards in Protein Structure Deck (35)
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1

What is the general structure of an amino acid?

A central carbon has an amino group, carboxyl group, a hydrogen atom and an R group covalently bonded to it

2

In what state are amino acids usually present as?

Zwitter Ions

3

What is an amino acid residue?

What remains of an amino acid after it has been joined by a peptide bond to form a protein

4

If an amino acid has a high PKA value what does that indicate?

It is a basic amino acid

5

What is pKa?

pKa tells you the strength of an acid, so how likely the groups are to lose or gain protons

6

If the pH is less than then pKa value what will happen to the side group?

The group is more likely to be protonated

7

What is the primary structure of a protein?

The amino acid sequence of the polypeptide chain

8

What is the secondary structure?

The way the chains fold into conformations like helices etc

9

What is the tertiary structure?

The overall 3D shape

10

What is the quaternary structure?

The association between different polypeptides to form a multi-subunit protein

11

In what type of reaction are peptide bonds formed?

A condensation reaction so a molecule of water is released

12

What does it mean by saying that peptide bonds are planar?

The atoms all lie in the same plane

13

Why can't peptide bonds rotate?

Electrons from the C=O bond of the carboxyl group move between the central carbon and nitrogen from the amino group giving it double bond properties (resonance)

14

Why do peptide bonds also have trans conformations?

By having the central carbon on opposite sides of the peptide bonds, the R groups will be further apart so won't repel

15

Why is the amino acid sequence important?

It determines the physical characteristic and the way in which the protein folds

16

What is the ISO electric point of a protein?

The pH at which there is no overall net charge

17

What happens if the pH is less than pI?

The amino acids will be protonated

18

What are conjugated proteins?

Proteins that are covantely linked to other chemical components as well as amino acids e.g. Glycoproteins

19

What binds hold the alpha helix structure together

Hydrogen bonds between the amino group and the carboxyl group

20

What 2 arrangements can be made from proteins with a beta sheet secondary structure?

Antiparallel and parallel sheets

21

Why are parallel beta sheets weaker than antiparallel sheets?

As the beta strands are running in the same direction the hydrogen bonds are at an angle and so are weaker

22

What is the domain of a globular protein?

Where part of a polypeptide chain folds into a distinct shape and often has a specific role

23

What are the 2 different types of tertiary structure?

Fibrous and Globular

24

How can amino acids be classified?

By whether they are:
-hydrophilic/hydrophobic
-polar/non-polar
-basic/acidic/neutral
-aliphatic/aromatic

25

If an amino acid has a charge will it be hydrophobic or hydrophilic

Hydrophilic

26

What does it mean if the pKa is equal to pH?

There will be equal amounts of protonated and deprotonated forms

27

What is the Henderson-Hasselbach equation?

pH = pKa + log(base/acid)

28

What bonds hold the tertiary structure together?

Ionic, H bonds, covalent, Van der Walls and hydrophobic and disulphide bonds

29

Between which amino acid residues do disulphide binds form?

Cystine

30

What properties do disulphide bonds give to proteins

The binds help keep the structure better so they can withstand hostile environments